Closed shyama-mama closed 8 months ago
I'm looking into the bug here. Seems to be when --skip_preprocessing is used.
nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit 6341f02
+| ✅ 159 tests passed |+
!| ❗ 20 tests had warnings |!
Not sure what the issue here is with linting. Unable to fix it automatically.
multiqc_config: 'assets/multiqc_config.yml' does not contain a matching 'report_comment'.
@shyama-mama I think the issue with the linting had to do with the new template that has been merged now. Could you resolve the conflicts? Then I can review again and we merge this, hopefully 🦾 😄
Would I have to add the test in this branch and push changes for the test to run here? Should I also add tests for sharding with bowtie2 and bwamem options for mapping?
Add the test here, and push and it will run on this branch, yes. But please don't add a new test, jut add sharding to any single mapper. We're trying to minimise the number of test commands ran cause things got out of hand in eager 2.*
@TCLamnidis Actually I realised I've got sharding enabled with 5000 reads as part of the 'test' profile in the config in this branch. So it has been running for all these tests. Would you rather have it added explicitly in the ci.yml with one of the tests?
oh right! Skimmed over that >.< nevermind me then. undo the ci.yml changes! all good
PR checklist
Added functionality to shard fastqs before aligning. This uses SeqKit. The sharded fastqs are merged together during the lane merge step.
scrape_software_versions.py
nf-core lint .
).nextflow run . -profile test,docker
).docs/usage.md
is updated.docs/output.md
is updated.CHANGELOG.md
is updated.README.md
is updated (including new tool citations and authors/contributors).